False Alarm on Hepatitis Virus Highlights Challenges of Pathogen Sleuthing

StephenW

                                False Alarm on Hepatitis Virus Highlights Challenges of Pathogen Sleuthing                                                                                        UCSF Researchers Find Virus from the Ocean That Confounds Lab Analysis                                                                                 Released:                                 9/25/2013 7:00 PM EDT                               
                                          Source Newsroom:                                                  University of California, San Francisco (UCSF)                                          more news from this source
                                                 
                        Newswise — The report by  scientists of a new hepatitis virus earlier this year was a false alarm,  according to UC San Francisco researchers who correctly identified the virus as  a contaminant present in a type of glassware used in many research labs. Their finding,  they said, highlights both the promise and peril of today’s powerful  “next-generation” lab techniques that are used to track down new agents of  disease.
In research  published online September 11, 2013, in the Journal of  Virology, researchers led by Charles Chiu, MD, PhD,  director of the UCSF Viral Diagnostics and Discovery Center, traced the source  of the contamination back to tiny diatoms, a type of oceanic algae having  nothing to do with human disease.
A scientific team  led by researchers from the National Institutes of Health (NIH) first  identified the virus as a potential cause of hepatitis in their study of blood samples from 92 people from  China who had serious cases of hepatitis not caused by any of the five known  hepatitis viruses. Chiu and colleagues discovered the same virus, which they  called parvovirus-like hybrid virus (PHV), independently, in a different set of  hepatitis patients whose disease was not caused by known viruses.
To further  investigate the origin of the virus, Chiu’s UCSF team tracked down its true  source by applying next-generation DNA sequencing techniques in a set of  carefully controlled experiments, and by referencing the ever-expanding  scientific databases that spell out and catalog viral genomes.
“At first we  thought this was a genuine hepatitis virus, but later we found it in data sets  from patients with many other diseases and even from animals,” said Chiu, a  professor of laboratory medicine at UCSF.
The researchers  also found that the virus sequenced from samples around the world strangely  exhibited almost no genomic diversity.   The research team strongly suspected that PHV was a laboratory  contaminant and began probing other databases in search of the true source of  the virus.
“We did some data  mining of environmental databases and found matching DNA sequences from viruses  originating in coastal waters off California and Oregon, but not elsewhere”  Chiu said.
A developer of  sampling and testing technologies may have sourced silica from diatoms in the  ocean to make a popular glass column used in the studies, Chiu said. The  columns are used to centrifugally spin biological samples to extract nucleic  acids — DNA and RNA.  Viral DNA that may  have once infected the diatoms was also likely extracted as a contaminant  during the procedure, along with DNA from biological samples, he said.
  “The silica used  in nearly all commercial spin columns is derived from the cell walls of  diatoms,” he said. “We believe that PHV may be a diatom virus that had  inadvertently contaminated the silica-based spin columns during  manufacture.”
The scientists do  not know what caused the cases of hepatitis examined in the studies.
Earlier techniques  developed to read out the sequence of DNA building blocks extracted from  biological samples permitted the stepwise decoding of genes and eventually the  characterization of entire genomes of humans and other organisms.
But in recent  years game-changing technological advances referred to as next-generation  sequencing  have permitted exponentially  faster and cheaper sequencing of millions of DNA molecules in a single run  through a lab protocol.
These  state-of-the-art techniques for piecing together the genomes of organisms from  tiny amounts of DNA can be used to efficiently detect pathogens previously  unknown to science, but they also are so sensitive that they easily pick up  contaminants, Chiu said.
It is not clear  why the NIH-led team did not also detect the contaminating DNA in the control  samples, Chiu said. Different techniques  may have been used in the analysis of control samples in comparison to  samples from hepatitis patients, or    there may have been lot-to-lot variations in glassware, Chiu speculates.
A similar viral  false-alarm scenario unfolded in recent years with a mouse virus called XMRV, first  reported in 2006. The virus initially was thought to be associated with human  prostate cancer and chronic fatigue syndrome, but last year Chiu and others,  including original XMRV co-discoverer Joseph DeRisi, PhD, Howard Hughes Medical  Institute Investigator and professor of biochemistry at UCSF, confirmed that XMRV was actually a viral contaminant of laboratory cell cultures and was not present in  prostate cancer tissue.
These studies  highlight the importance of repeating experiments with good controls to ensure  that results are accurate, Chiu said. “Reproducibility is a cornerstone of  science, yet far too few studies are validated by follow-up investigation,” he said.  Next-generation sequencing is a promising  approach to rapidly confirm and validate discoveries of new disease agents,  saving investments in time and money that might otherwise be spent pursuing  false leads, he added.
UCSF is a leading  university dedicated to promoting health worldwide through advanced biomedical  research, graduate-level education in the life sciences and health professions,  and excellence in patient care. It includes top-ranked graduate schools of  dentistry, medicine, nursing and pharmacy, a graduate division with nationally  renowned programs in basic biomedical, translational and population sciences,  as well as a preeminent biomedical research enterprise and two top-ranked  hospitals, UCSF Medical Center and UCSF Benioff Children’s Hospital.
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